Run hypergeometric gene enrichment analysis.

Run hypergeometric gene enrichment analysis.

runHG(
  gene.list,
  gene.universe,
  species,
  pathway.db = "Bader",
  n.workers = 16,
  my.pathway = NULL,
  my.pathway.representation = "ENTREZ",
  min.size = 2,
  max.size = 300,
  e2s = F,
  go.ontology = "BP",
  verbose = T
)

Arguments

gene.list

Named list of genesets to run enrichment on (symbol format).

gene.universe

Gene universe (symbol format)

species

Species. One of "Mm" (mouse) or "Hs" (human)

pathway.db

Name of databse to get annotation genelists from. Default is "Bader". See scMiko::getAnnotationPathways() for options.

n.workers

Number of workers for parallelization. Default is 16.

my.pathway

Named list of pathways, with each entry containing vector of Entrez IDs. Retrieved internally unless explicitly provided.

my.pathway.representation

If my.pathway is provided, species which format, options = "SYMBOL" or "ENTREZ". ENTREZ is Default.

min.size

min geneset size. Default is 2.

max.size

max geneset size. Default is 300.

e2s

entrez to symbol mapping (computationally demanding). Default False.

go.ontology

BP, MF or CC. Ignored if pathway.db != "GO".

verbose

Print progress. Default is TRUE.

Value

enrichment results

Author

Nicholas Mikolajewicz